Helpers and Other Conventions

I believe the goal is to avoid name conflicts.

Its good goal but 1 avoid of conflicts should not create others..
Helper is too common word as Config which is used already for namespace.. 
And having CodeIgniter, App, Config, Helper namespaces just within 1 sample app its too much I think..

At least for Functions I don't see any problem to have them just under CodeIgniter namespace. 
Perhaps some system option to alias them into the APP namespace can be helpful.

By the way many calls of USE (in controllers / models / views ) is something common this days. 
My IDE PHPstorm even auto add it at the start of the file when you are using some class/function under some namespace..

So this is the way how PHP is made and developers must accept it I think.

Best VPS Hosting : Digital Ocean